Well, my two (one is obivous, the other not-so-obvious), but here I go:

1. CJC's Ganon Battle: By far the most innovative battle I've seen, acts a lot like Link's Awakening, and uses classic sprites. I am going to be implementing that pretty soon.

2. (If I may have your permission @Imzogelmo ), the Mini-Dodongos. They were a pretty cool minor enemy that might have some use in varying the enemy list a bit.